From fda8f381439fa7514547ebbee20b13031eb51564 Mon Sep 17 00:00:00 2001 From: NanoCell Interactions Lab Date: Tue, 10 Feb 2026 15:04:38 -0500 Subject: [PATCH 1/5] fix(pipeline): default file/folder naming to 'No' --- 3DFISHinCelegans/NewFishPureCP.cppipe | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/3DFISHinCelegans/NewFishPureCP.cppipe b/3DFISHinCelegans/NewFishPureCP.cppipe index 812df0939..8b3e35928 100755 --- a/3DFISHinCelegans/NewFishPureCP.cppipe +++ b/3DFISHinCelegans/NewFishPureCP.cppipe @@ -1,6 +1,6 @@ CellProfiler Pipeline: http://www.cellprofiler.org Version:5 -DateRevision:421 +DateRevision:428 GitHash: ModuleCount:20 HasImagePlaneDetails:False @@ -251,7 +251,7 @@ SaveImages:[module_num:19|svn_version:'Unknown'|variable_revision_number:16|show ExportToSpreadsheet:[module_num:20|svn_version:'Unknown'|variable_revision_number:13|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] Select the column delimiter:Comma (",") Add image metadata columns to your object data file?:No - Add image file and folder names to your object data file?:Yes + Add image file and folder names to your object data file?:No Select the measurements to export:Yes Calculate the per-image mean values for object measurements?:No Calculate the per-image median values for object measurements?:No From d7c548d499440a07f34330aa5be619c7f5dc266e Mon Sep 17 00:00:00 2001 From: labnanocell <166658616+labnanocell@users.noreply.github.com> Date: Wed, 11 Feb 2026 13:19:46 -0500 Subject: [PATCH 2/5] Update Nuclei3DTimeConsumingPipeline.md --- .../docs/source/3DNuclei/Nuclei3DTimeConsumingPipeline.md | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/internal_use/docs/source/3DNuclei/Nuclei3DTimeConsumingPipeline.md b/internal_use/docs/source/3DNuclei/Nuclei3DTimeConsumingPipeline.md index a4598a14a..3e92dd5e3 100644 --- a/internal_use/docs/source/3DNuclei/Nuclei3DTimeConsumingPipeline.md +++ b/internal_use/docs/source/3DNuclei/Nuclei3DTimeConsumingPipeline.md @@ -19,8 +19,6 @@ and the clustering of their nuclei in 3D cell culture. Voxel dimensions: 0.124x0.124x0.200 um -Calibration Image: Voxel dimensions: 1x1x1 um - ## **Importing data in CellProfiler** 1. Highlight the **Images** module. @@ -56,8 +54,7 @@ always a good practice to check if everything is fine. >The relative pixel spacing was provided and is 0.124 um in x and y and -0.200 um in z. To run the calibration file please change the relative -pixel spacing to 1x1x1 um. +0.200 um in z. 6. Assign the images “variable names” that describe the contents in the image. For example, use the name "Nuclei", "DNA", “DAPI” or something else that will remind you what the image is. 7. Hit the "update" button to populate From e646cd26c6338355c842d62ef10f6f5a2af06233 Mon Sep 17 00:00:00 2001 From: labnanocell <166658616+labnanocell@users.noreply.github.com> Date: Thu, 12 Feb 2026 11:42:42 -0500 Subject: [PATCH 3/5] Update BBBC022_QualityControlExercise.md --- .../source/QualityControl/BBBC022_QualityControlExercise.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/internal_use/docs/source/QualityControl/BBBC022_QualityControlExercise.md b/internal_use/docs/source/QualityControl/BBBC022_QualityControlExercise.md index 341e993ce..38ecbf3ff 100644 --- a/internal_use/docs/source/QualityControl/BBBC022_QualityControlExercise.md +++ b/internal_use/docs/source/QualityControl/BBBC022_QualityControlExercise.md @@ -204,7 +204,7 @@ in later steps. *Figure 1: Examining the objects inside a gate.* ``` -- Look at some of the images inside the gate ( you may need to click +- Look at some of the images inside the gate (you may need to click ‘Show controls’ to adjust the zoom, contrast stretch, etc). Are they in focus, and are they free of bright debris? If they seem all or mostly like they’re high quality, adjust the gate to look at a From c84f5316ff5a2264c6f15880e6c917f602bf4666 Mon Sep 17 00:00:00 2001 From: labnanocell <166658616+labnanocell@users.noreply.github.com> Date: Thu, 12 Feb 2026 11:44:25 -0500 Subject: [PATCH 4/5] Update BBBC022_QualityControlExercise.md --- .../source/QualityControl/BBBC022_QualityControlExercise.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/internal_use/docs/source/QualityControl/BBBC022_QualityControlExercise.md b/internal_use/docs/source/QualityControl/BBBC022_QualityControlExercise.md index 38ecbf3ff..e36b2d239 100644 --- a/internal_use/docs/source/QualityControl/BBBC022_QualityControlExercise.md +++ b/internal_use/docs/source/QualityControl/BBBC022_QualityControlExercise.md @@ -211,7 +211,7 @@ in later steps. different/smaller subset or delete it altogether by using the Gate Inspector (‘gate’-> ‘MANAGE GATES’). -## 4. **Optional- use the PlateViewer tool to check for other features to gate on (~10 minutes)** +## 4. **Optional — use the PlateViewer tool to check for other features to gate on (~10 minutes)** If you want to see if you can find additional features that might distinguish good images from bad images, feel free to explore the feature set more thoroughly. From 3f053dcfeaa5a11217bdcb9a4bd9809642618ca0 Mon Sep 17 00:00:00 2001 From: labnanocell <166658616+labnanocell@users.noreply.github.com> Date: Thu, 12 Feb 2026 16:54:30 -0500 Subject: [PATCH 5/5] Update UnmixColorsTutorial.md --- .../docs/source/UnmixColorsTutorial/UnmixColorsTutorial.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/internal_use/docs/source/UnmixColorsTutorial/UnmixColorsTutorial.md b/internal_use/docs/source/UnmixColorsTutorial/UnmixColorsTutorial.md index 5e77389a6..96149d16c 100644 --- a/internal_use/docs/source/UnmixColorsTutorial/UnmixColorsTutorial.md +++ b/internal_use/docs/source/UnmixColorsTutorial/UnmixColorsTutorial.md @@ -38,8 +38,7 @@ absorbance in the Custom mode. ## **Materials necessary for this exercise:** -- Histopathological image of parathyroid adenoma. Hematoxylin and eosin - : stain in a slide. +- Histopathological image of parathyroid adenoma. Hematoxylin and eosin: stain in a slide. **Example 1:** Parathyroid Adenoma